[gmx-users] virtual sites in reference structure

[Ahmet yıldırım]

Dear Tsjerk,

Do the virtual sites cause incorrect calculations of SASA, RMSD or something
else?

Regards
2013/2/21 Tsjerk Wassenaar <tsjerkw at gmail.com>

> Hi Ahmet,
>
> You can always use suitable index groups for analysis.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Feb 21, 2013 at 7:08 AM, Ahmet yıldırım <ahmedo047 at gmail.com>
> wrote:
> > I thought the virtual sites can affect analysis.For example, dont they
> cause
> > incorrect calculations of SASA, RMSD or something else?
> >
> > Thanks in advance
> >
> > 2013/2/20 Justin Lemkul <jalemkul at vt.edu>
> >
> >>
> >>
> >> On 2/20/13 9:18 AM, Ahmet yıldırım wrote:
> >>
> >>> Dear users,
> >>>
> >>> I have the virtual sites in reference structure and all trajectory.
> When
> >>> analyzing simulation, do I have to get rid of those(virtual sites)? If
> >>> yes/no, why?
> >>>
> >>>
> >> Why do you think you need to remove them?
> >>
> >> -Justin
> >>
> >> --
> >> ==============================**==========
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Research Scientist
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >>
> >> ==============================**==========
> >> --
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> >
> >
> >
> > --
> > Ahmet Yıldırım
> > --
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Biocomputing Group
> Department of Biological Sciences
> 2500 University Drive NW
> Calgary, AB T2N 1N4
> Canada
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-- 
Ahmet Yıldırım